From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 25 Mar 2016 14:52:04 +0000 (+0000)
Subject: JAL-2034 make colour scheme update optional when group conservation is calculated... 
X-Git-Tag: Release_2_10_0~120^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=88d5ff9b60bc7c99a427c2d6fc9d04823e185d68;p=jalview.git

JAL-2034 make colour scheme update optional when group conservation is calculated, and pass back a ‘change’ flag
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c9afec7..ee4d7c2 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -504,14 +504,31 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * calculate residue conservation for group - but only if necessary.
+   * calculate residue conservation and colourschemes for group - but only if
+   * necessary. returns true if the calculation resulted in a visible change to
+   * group
    */
-  public void recalcConservation()
+  public boolean recalcConservation()
+  {
+    return recalcConservation(false);
+  }
+
+  /**
+   * calculate residue conservation for group - but only if necessary. returns
+   * true if the calculation resulted in a visible change to group
+   * 
+   * @param defer
+   *          when set, colourschemes for this group are not refreshed after
+   *          recalculation
+   */
+  public boolean recalcConservation(boolean defer)
   {
     if (cs == null && consensus == null && conservation == null)
     {
-      return;
+      return false;
     }
+    // TODO: try harder to detect changes in state in order to minimise
+    // recalculation effort
     try
     {
       Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
@@ -545,16 +562,22 @@ public class SequenceGroup implements AnnotatedCollectionI
           }
         }
       }
-      if (cs != null)
+      if (cs != null && !defer)
       {
+        // TODO: JAL-2034 should cs.alignmentChanged modify return state
         cs.alignmentChanged(context != null ? context : this, null);
+        return true;
+      }
+      else
+      {
+        return false;
       }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
-
+    return false;
   }
 
   private void _updateConservationRow(Conservation c)